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@bioexcel

BioExcel

Center of Excellence for Computational Biomolecular Research

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  1. biobb biobb Public

    Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

    Python 56 8

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 46 20

  3. gromacs-2022-cp2k-tutorial gromacs-2022-cp2k-tutorial Public

    Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface

    Makefile 34 7

  4. cp2K_qmmm_tutorials_for_biological_simulations cp2K_qmmm_tutorials_for_biological_simulations Public

    Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.

    Jupyter Notebook 22 7

  5. biobb_structure_checking biobb_structure_checking Public

    Python 11 1

  6. biobb_amber biobb_amber Public

    Biobb_amber is a BioBB category for AMBER MD package.

    Python 11 3

Repositories

Showing 10 of 119 repositories
  • biobb Public

    Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

    bioexcel/biobb’s past year of commit activity
    Python 56 Apache-2.0 8 0 0 Updated Mar 11, 2025
  • biobb_structure_checking Public
    bioexcel/biobb_structure_checking’s past year of commit activity
    Python 11 Apache-2.0 1 2 1 Updated Feb 25, 2025
  • biobb_mem Public
    bioexcel/biobb_mem’s past year of commit activity
    Python 0 Apache-2.0 0 1 0 Updated Feb 10, 2025
  • biobb_common Public

    Biobb_common is the base package required to use the biobb packages.

    bioexcel/biobb_common’s past year of commit activity
    Python 0 Apache-2.0 1 3 0 Updated Feb 7, 2025
  • biobb_workflows Public

    Global repository for all the BioExcel Building Blocks Workflows

    bioexcel/biobb_workflows’s past year of commit activity
    Common Workflow Language 4 2 0 0 Updated Jan 28, 2025
  • biobb_analysis Public

    Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.

    bioexcel/biobb_analysis’s past year of commit activity
    Python 4 Apache-2.0 2 0 0 Updated Jan 28, 2025
  • biobb_vs Public

    Biobb_vs is the Biobb module collection to perform virtual screening studies.

    bioexcel/biobb_vs’s past year of commit activity
    Python 1 Apache-2.0 2 0 0 Updated Jan 28, 2025
  • biobb_structure_utils Public

    Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.

    bioexcel/biobb_structure_utils’s past year of commit activity
    Python 2 Apache-2.0 3 1 0 Updated Jan 28, 2025
  • biobb_pytorch Public

    Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.

    bioexcel/biobb_pytorch’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Jan 28, 2025
  • biobb_pdb_tools Public
    bioexcel/biobb_pdb_tools’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Jan 28, 2025
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